Dear developers,
How are you?
I have a question about scale bar. I am not completely sure that the scale bar I drew is correct.
What are the scale settings for drawing the scale bar?
By the default the scale bar is in Angstroms isn’t it?
In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc)
Is there the same possibility in Chimera?
Thank you
Sincerely,
Dmitry
Dear Dmitry, Pretty good - I hope you are well too!
The scale bar length and thickness are in the physical distance units of your data, whatever those are. If your structure is in angstroms, they will be in angstroms, but if your map is in nanometers, they will be in nanometers.
I'm not sure what your question is about the other settings, but we try to explain them all in the help, which you can see by clicking the Help button or viewing the copy at our website: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.html
I don't think there is a control for scalebar pixels per unit distance. I found a post from 2005 with python for setting the pixels per unit distance in the whole graphics window (not the scale bar), but I don't know if it would work with today's Chimera: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-May/000369.html
One thing to keep in mind is that the scale bar is an object in 3 dimensions, so you want it at a similar depth to your structures and maps, because due to perspective, if it is in front it will look larger, if towards the back it will look smaller. You may be able to see its depth in the Side View, or by rotating the main view 90 degrees (and then putting it back, of course), e.g. commands:
turn y 90 turn y -90
Another possibility is to turn off perspective, instead using orthographic projection:
set projection ortho set proj persp
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 17, 2015, at 3:56 AM, Dmitry semchonok@gmail.com wrote:
Dear developers, How are you?
I have a question about scale bar. I am not completely sure that the scale bar I drew is correct.
What are the scale settings for drawing the scale bar?
By the default the scale bar is in Angstroms isn’t it?
In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc)
Is there the same possibility in Chimera? Thank you Sincerely, Dmitry
Dear All,
Will you please tell me how to measure the distance between 2 spots of the EM map? It seems the way of scale bar does not work.
Smith
At 2015-03-18 01:44:52, "Elaine Meng" meng@cgl.ucsf.edu wrote:
Dear Dmitry, Pretty good - I hope you are well too!
The scale bar length and thickness are in the physical distance units of your data, whatever those are. If your structure is in angstroms, they will be in angstroms, but if your map is in nanometers, they will be in nanometers.
I'm not sure what your question is about the other settings, but we try to explain them all in the help, which you can see by clicking the Help button or viewing the copy at our website: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.html
I don't think there is a control for scalebar pixels per unit distance. I found a post from 2005 with python for setting the pixels per unit distance in the whole graphics window (not the scale bar), but I don't know if it would work with today's Chimera: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2005-May/000369.html
One thing to keep in mind is that the scale bar is an object in 3 dimensions, so you want it at a similar depth to your structures and maps, because due to perspective, if it is in front it will look larger, if towards the back it will look smaller. You may be able to see its depth in the Side View, or by rotating the main view 90 degrees (and then putting it back, of course), e.g. commands:
turn y 90 turn y -90
Another possibility is to turn off perspective, instead using orthographic projection:
set projection ortho set proj persp
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 17, 2015, at 3:56 AM, Dmitry semchonok@gmail.com wrote:
Dear developers, How are you?
I have a question about scale bar. I am not completely sure that the scale bar I drew is correct.
What are the scale settings for drawing the scale bar?
By the default the scale bar is in Angstroms isn’t it?
In ImageJ there is a possibility to set the scale 1 pixel = X value (nm/Å/etc)
Is there the same possibility in Chimera? Thank you Sincerely, Dmitry
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Smith, For measuring the distance between two points on an isosurface, the better approach is to place markers on those points and then measure the distance between them. For details, please see this previous post:
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010609.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 26, 2015, at 11:19 PM, Smith Liu smith_liu123@163.com wrote:
Dear All,
Will you please tell me how to measure the distance between 2 spots of the EM map? It seems the way of scale bar does not work.
Smith
participants (3)
-
Dmitry -
Elaine Meng -
Smith Liu